Le Petite Madison comes to mind. I'm sure there are loads more too.

http://www.gayot.com/restaurants/best-newyork-ny-top10-romanticrestaurant_1ny.html

they have dog friendly romantic restaurants now which is something new I never saw... How that gets on that list shocks me... lol

Some of my very intimate, romantic and memorable dinners in Manhattan...

Not in this particular order. Enjoy!

Definitely:
One if by Land, Two if by Sea (West Village)- Unique.
Merimoto (Chelsea) - Creative Japanese.
Le Bernardin (Midtown West) - Exquisite.
Asiate (Columbus Circle) - Beautiful views.
The Four Seasons (Midtown East) - The Pool Room. Delicious!

Maybe:
Chez Josephine (Hell's Kitchen) - Intimate and very colorful.
Le Cirque (Midtown) - Playful.

Power Breakfast:
The Library at Loews Regency Hotel.

View

Per Se

Le Bernardin

Auriole